//
// Manta - Structural Variant and Indel Caller
// Copyright (c) 2013-2019 Illumina, Inc.
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program.  If not, see <http://www.gnu.org/licenses/>.
//
//

/// \file
/// \author Chris Saunders
///

#include "manta/JunctionIdGenerator.hpp"

void JunctionIdGenerator::getId(const EdgeInfo& edge, const SVCandidate& sv, const bool isRNA, SVId& svId)
{
  using namespace EXTENDED_SV_TYPE;

  svId.svType = (getExtendedSVType(sv, isRNA));

  svId.localId =
      str(_SVIdFormatter % label(svId.svType) % edge.locusIndex % edge.nodeIndex1 % edge.nodeIndex2 %
          sv.candidateIndex % sv.assemblyAlignIndex % sv.assemblySegmentIndex);

  if (isSVTransloc(svId.svType) || isSVInv(svId.svType)) {
    svId.mateId  = svId.localId + ":1";
    svId.localId = svId.localId + ":0";
  } else {
    svId.mateId.clear();
  }
}
